Tag: PPI

Bioconductor – BioNERO

DOI: 10.18129/B9.bioc.BioNERO     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BioNERO. Biological Network Reconstruction Omnibus Bioconductor version: 3.15 BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses…

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NetworkAnalyst

Starting from a list of gene IDs with optional expression values Starting from a single count table (RNAseq) or intensity table (microarray) Starting with several gene expression tables for meta-analysis Uploading raw RNAseq files (any species) for mapping & quantification Starting with a network file (sif, graphml, json) News &…

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Exploration of the role of oxidative stress-related genes in LPS-induced acute lung injury via bioinformatics and experimental studies

Selection of 152 ALI-related genes (ALIRGs) by weighted gene co-expression network analysis (WGCNA) The samples of the GSE16409, GSE18341 and GSE102016 datasets were discretely distributed before merging, and the sample data (ALI = 21 and control = 14) was uniform after batch processing (Supplementary Fig. 1a,b). To identify the ALIRGs, the WGCNA was performed in…

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Key Genes for Pyroptosis-induced Salivary Gland Inflammation

Kaiyuan Zhang,1,* Ziyue Luo,1,* Xinchao Zhu,1 Xinyi Yao,1 Dingqi Lu,2 Liying Chen,1 Tao Hong,1 Yating Ren,1 Xinchang Wang3 1Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China; 2First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China;…

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next-generation AI docking that beats DiffDock and AlphaFold-latest

Receptor.AI has announced the ArtiDock – the best-in-class model for “AI docking”, which predicts the binding poses of small molecule ligands in protein binding pockets with unprecedented speed and accuracy. We performed a comprehensive comparison of ArtiDock with the best modern AI docking techniques and with the most widely used conventional…

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Music compensates for altered gene expression in age-related cognitive disorders

Global impact of music on the human transcriptome We first aimed at quantifying the global effect of music on the transcriptomes of the two groups of donors separately. ACD patients exposed to music showed 2.3 times more DEGs (n = 2605) than controls (n = 1148); Table 2. Moreover, while the proportion up-regulated/down-regulated DEGs…

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Gastroenterology Month in Review: November 2023

Although 2023 is almost over, the field of gastroenterology shows no signs of slowing down as the year comes to a close. The month of November was a busy one, characterized by an FDA approval for erosive esophagitis, the discontinuation of a phase 3 program for ulcerative colitis, and news…

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Cellular senescence triggers intracellular acidification and lysosomal pH alkalinized via ATP6AP2 attenuation in breast cancer cells

Doxo and Abe promote cellular senescence accompanied by an altered profile of senescence-related genes in breast cancer cells Doxo and Abe were used to treat breast cancer cells (human triple-negative breast cancer cell line MDA-MB-231 and human luminal A subtype breast cancer cell line MCF-7) for 24 h, without a robust…

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COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma | BMC Gastroenterology

Bioinformatics analysis The GEO database (www.ncbi.nlm.nih.gov/geo/) provided detailed gene expression information for the GSE62165 microarray. Differentially expressed genes were identified using the online tool Morpheus (software.broadinstitute.org/morpheus/) (fold change = normal pancreatic tissue gene expression/PDAC tissue gene expression, P value < 0.05 and |log2(fold change)|>1). The downstream analysis was based on the genes with the…

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Inhibition of providencia vermicola FabD

Introduction Microbial resistance has become a problem in the contemporary medical environment due to the inadequate development of new antibiotics and the asinine prescription of antibiotics in both developed and developing nations. Antimicrobial resistance (AMR), which affects wealthy and developing nations, is a global concern.1 AMR is a problem for…

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Bioinformatics analysis of immune cell infiltration patterns and potential diagnostic markers in atherosclerosis

A database in the Gene Set Enrichment Analysis (GSEA; www.gsea-msigdb.org/gsea/msigdb/index.jsp) platform10,11 was used to identify 134 GLN metabolism-associated genes. Weighted gene co-expression network analysis (WGCNA) and module screening GLN-associated gene sets were investigated using WGCNA. The results demonstrated that when the weighted value was 24 (Fig. 1A), scale independence was greater…

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Breakthrough offers a new way to stop AI ‘hallucinating’ and making up facts

Could this breakthrough deal with the problem of AI ‘hallucination’? (Getty Images) (peepo via Getty Images) A technological breakthrough could help to deal with the problem of artificial intelligence ‘hallucination’, wherein AI models, including chat bots, sometimes make things up or present false answers. AI is beginning to be used…

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Expression profiles of circRNAs and biomarkers for COPD

Introduction Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease featured by airflow obstruction with high prevalence, morbidity, and mortality. It is reported that COPD is the third leading cause of death globally at present, and the incidence of COPD in adults over 40 years is more than…

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Eight biotech companies tackling infectious diseases head-on

Infectious diseases are diseases that are caused by pathogens that enter the body, hijack the body’s immune system and multiply, causing an infection. Five of the deadliest infectious diseases are measles, tuberculosis, malaria, diarrhoeal disease and influenza, according to the World Economic Forum. While Our World in Data statistics suggest…

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Identification of circRNA-miRNA-mRNA network as biomarkers for interstitial cystitis/bladder pain syndrome

Research Paper Advance Articles Shi-Qin Yang1, *, , Liao Peng1, *, , Le-De Lin1, , Yuan-Zhuo Chen1, , Meng-Zhu Liu1, , Chi Zhang1, , Jia-Wei Chen1, , De-Yi Luo1, , 1 Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China * Equal contribution…

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2023-11-03 | NDAQ:TVTX | Press Release

Two-year results from both PROTECT and DUPLEX pivotal Phase 3 studies demonstrate treatment with sparsentan has the potential to preserve kidney function and significantly delay time to kidney failure, suggesting long-term benefits in IgAN and FSGS In PROTECT, the only head-to-head study conducted to date in IgAN, FILSPARI&circledR; (sparsentan) showed…

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Travere Therapeutics Announces Late-Breaking Data from Phase 3 Studies of Sparsentan in IgAN and FSGS Published in The Lancet and The NEJM Respectively and Presented at the American Society of Nephrol

Two-year results from both PROTECT and DUPLEX pivotal Phase 3 studies demonstrate treatment with sparsentan has the potential to preserve kidney function and significantly delay time to kidney failure, suggesting long-term benefits in IgAN and FSGS In PROTECT, the only head-to-head study conducted to date in IgAN, FILSPARI® (sparsentan) showed…

Continue Reading Travere Therapeutics Announces Late-Breaking Data from Phase 3 Studies of Sparsentan in IgAN and FSGS Published in The Lancet and The NEJM Respectively and Presented at the American Society of Nephrol

Genomic disturbance of vitellogenin 2 (vtg2) leads to vitellin membrane deficiencies and significant mortalities at early stages of embryonic development in zebrafish (Danio rerio)

A large deletion mutation of 2811 bp of gDNA was introduced into zebrafish vtg2 via CRISPR/Cas9 genome editing. A schematic representation of the general strategy for CRISPR target design and application is given in Fig. 1A–C. The introduced deletion involved 1692 bp of the vtg2 transcript, encoding 564 aa of its respective protein, and…

Continue Reading Genomic disturbance of vitellogenin 2 (vtg2) leads to vitellin membrane deficiencies and significant mortalities at early stages of embryonic development in zebrafish (Danio rerio)

Topological links in predicted protein complex structures reveal limitations of AlphaFold

Identification of topological links in protein complexes To demonstrate why new algorithms are needed to identify topological links in protein‒protein complex structures, we applied existing methods to 4 structures predicted by AlphaFold-Multimer v2.2.0 (Fig. 1a–d) and 4 experimental complex structures from the Protein Data Bank (PDB, Fig. 2a–d). For these 4 experimental…

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Identification of hub genes associated with gastric cancer

Introduction GC is a common malignant tumor of digestive system. According to the International Agency for Research on Cancer (IARC) of the World Health Organization, there were 19.29 million new cancer cases and 9.96 million deaths worldwide in 2020, of which the number of new cases of GC was 1089,103…

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Expanding causal genes for Parkinson’s disease via multi-omics analysis

Proteins causally associated with PD in the brain MR analysis of brain dorsolateral prefrontal cortex (dlPFC) pQTLs identified six genetically determined significant proteins on PD after multiple testing corrections (P < 8.55E-05 (0.05/585)). Specifically, the increased abundance of 3 proteins was significantly associated with an increased risk of PD, including GPNMB (OR:1.464,…

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A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

A computational protocol, CaseOLAP LIFT, and a use case are presented for investigating mitochondrial proteins and their associations with cardiovascular disease as described in biomedical reports. This protocol can be easily adapted to study user-selected cellular components and diseases. This computational protocol is significant because it allows a work to…

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PPI training: involving patients and the public in your research

We recognise the importance of training researchers to involve patients and the public meaningfully in their research. Our co-produced specialist patient and public involvement (PPI) training, which we develop and deliver in partnership with public contributors and tailor to individual projects, provides practical tools and role-models inclusive approaches needed to…

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Identification of a lncRNA/circRNA-miRNA-mRNA ceRNA Network in Alzheimer’s Disease

Background: Alzheimer’s disease (AD) occurs in the elderly and pre-elderly, characterized by decline of memory, cognitive dysfunction, impairment of learning capacity, and motor dysfunction. Recently a competitive endogenous RNA (ceRNA) network has been found to be related to AD progression, but there is still little understanding of the ceRNA regulatory…

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Toxins | Free Full-Text | Smart-seq2 Technology Reveals a Novel Mechanism That Zearalenone Inhibits the In Vitro Maturation of Ovine Oocytes by Influencing TNFAIP6 Expression

Figure 1. ZEN concentration screening and transcriptome data validation. (A) The growth status of sheep oocytes cultured in vitro after 36 h of exposure to different concentrations of ZEN(CK,10 μM, 20 μM, and 30 μM) (10×, 100 μm), (B) qRT-PCR results of SOD1, CCNB1, GPX1, CAT, CDK1, and SOD2 in…

Continue Reading Toxins | Free Full-Text | Smart-seq2 Technology Reveals a Novel Mechanism That Zearalenone Inhibits the In Vitro Maturation of Ovine Oocytes by Influencing TNFAIP6 Expression

PHF5A is a potential diagnostic, prognostic, and immunological biomarker in pan-cancer

PHF5A expression analysis Figure 1A demonstrated that PHF5A expression level was compared between tumor and corresponding normal tissues using TIMER2 tool. As compared to normal tissues, PHF5A expression was considerably elevated in Bladder urothelial carcinoma (BLCA), Breast invasive carcinoma (BRCA), Cholangiocarcinoma (CHOL), Colon adenocarcinoma (COAD), Esophageal carcinoma (ESCA), Head and neck…

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Protein protein interactions classification

Protein protein interactions classification 0 I did protein protein interaction analysis by CellPhoneDB. Now, I want to classify the results based on biological function. Does anyone know or can suggest any package or web tool to do this? PPI protein-protein-interaction • 21 views • link updated 1 hour ago by…

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2023-10-13 | NDAQ:TVTX | Press Release

Two late-breaking high-impact oral presentations of the Phase 3 PROTECT Study of FILSPARI&circledR;(sparsentan) in IgAN and Phase 3 DUPLEX Study of sparsentan in FSGS 11 total abstracts accepted for presentation highlight Travere&CloseCurlyQuote;s leadership and commitment in the field of rare kidney disease SAN DIEGO, Oct. 13, 2023 (GLOBE NEWSWIRE) —…

Continue Reading 2023-10-13 | NDAQ:TVTX | Press Release

Travere Therapeutics to Present Abstracts at the American

Two late-breaking high-impact oral presentations of the Phase 3 PROTECT Study of FILSPARI® (sparsentan) in IgAN and Phase 3 DUPLEX Study of sparsentan in FSGS 11 total abstracts accepted for presentation highlight Travere’s leadership and commitment in the field of rare kidney disease SAN DIEGO, Oct. 13, 2023 (GLOBE NEWSWIRE)…

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Travere Therapeutics to Present Abstracts at the American Society of Nephrology (ASN) Kidney Week 2023

Travere Therapeutics to Present Abstracts at the American Society of Nephrology (ASN) Kidney Week 2023 Two late-breaking high-impact oral presentations of the Phase 3 PROTECT Study of FILSPARI ® (sparsentan) in IgAN and Phase 3 DUPLEX Study of sparsentan in FSGS 11 total abstracts accepted for presentation highlight Travere’s leadership…

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Signatures of necroptosis-related genes as diagnostic markers of endometriosis and their correlation with immune infiltration | BMC Women’s Health

Technical roadmap Figure 1. Fig. 1 Analysis of endometriosis-related differentially expressed genes Using the limma package, we first normalized the expression profile data of the endometriosis datasets, GSE7305 and GSE11691. The data distribution before and after standardized treatment is revealed in a box plot (Figs. 2A–D). We found that the data after…

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Virulence Characteristics of Salmonella Enteritidis

Introduction As an important zoonosis pathogen, Salmonella is widely distributed in nature and one of the four major pathogens causing global diarrhea diseases.1 Salmonella has six subspecies and 2659 serotypes, among which Salmonella Enteritidis (S. Enteritidis) are the most common serotypes causing Salmonella outbreaks.1 S. Enteritidis has a wide variety…

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Plants | Free Full-Text | In Silico RNAseq and Biochemical Analyses of Glucose-6-Phosphate Dehydrogenase (G6PDH) from Sweet Pepper Fruits: Involvement of Nitric Oxide (NO) in Ripening and Modulation

Figure 1. Genomic organization of the CaG6PDH gene family. The gene structure is displayed with exons (green boxes) and introns (black lines). Untranslated regions are shown in grey boxes. Exon–intron regions are drawn at scale. Figure 1. Genomic organization of the CaG6PDH gene family. The gene structure is displayed with…

Continue Reading Plants | Free Full-Text | In Silico RNAseq and Biochemical Analyses of Glucose-6-Phosphate Dehydrogenase (G6PDH) from Sweet Pepper Fruits: Involvement of Nitric Oxide (NO) in Ripening and Modulation

Elucidating the molecular mechanisms underlying anti-inflammatory effects of Morchella esculenta in the arachidonic acid metabolic pathway by network pharmacology and molecular docking

Identification of the anti-inflammatory target of active ingredients in Morchella esculenta The active ingredient of “Morchella esculenta” according to the NPASS database was (E)-Octadec-11-En-9-Yinoic Acid (EOYA) (Fig. 1), numbered NPC179764, with a chemical formula of C18H30O2, and ‘SMILE’ value, CCCCCC/C=C/C#CCCCCCCCC(=O)O. The targets obtained by searching the “EOYA Smile Value” in the…

Continue Reading Elucidating the molecular mechanisms underlying anti-inflammatory effects of Morchella esculenta in the arachidonic acid metabolic pathway by network pharmacology and molecular docking

Study on potential differentially expressed genes in idiopathic pulmonary fibrosis by bioinformatics and next generation sequencing data analysis

Abstract Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the…

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Travere Therapeutics Announces Confirmatory Data from the

FILSPARI® (sparsentan) achieved a clinically meaningful difference vs. irbesartan in eGFR total slope (1.0 mL/min/1.73m2 per year) [p= 0.058] and eGFR chronic slope (1.1 mL/min/1.73m2 per year) [p=0.037]. Patients treated with FILSPARI over two years exhibited one of the slowest annual rates of kidney function decline seen in a clinical…

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Total Flavonoids of Rhizoma Drynariae Treat Osteoarthritis

Introduction Osteoarthritis (OA) is a common degenerative joint disease characterized by chronic pain and ambulation limitation, affecting about 250 million people worldwide.1 With increased aging population, the OA incidence rapidly increases and OA has become a major cause of disability.2,3 The morbidity of OA is closely related to articular cartilage,…

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Association analysis of agronomic traits and construction of genetic networks by resequencing of 306 sugar beet (Beta vulgaris L.) lines

Genome resequencing approach for genotyping 306 sugar beet germplasm resources In this study, we performed high-depth genome-wide resequencing of 306 sugar beet accessions using an Illumina HiSeq 2000 sequencer, obtaining 1977.12 Gb of sequencing data. This collection included 72 endemic accessions from Northeast China (Harbin), 114 endemic accessions from North China…

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Ferroptosis-related factors in the substantia nigra are associated with Parkinson’s disease

Cell types and their proportion in the SN of PD patients Based on the cell annotation results on the Single Cell Portal uploaded by Prof. Macosko’s group, cells were extracted and classified into different types from human SN samples (Fig. 1A). After 135,344 cells were extracted from 34 PD samples and…

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Bioconductor – magrene

DOI: 10.18129/B9.bioc.magrene   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see magrene. Motif Analysis In Gene Regulatory Networks Bioconductor version: 3.16 magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and…

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[Protein-Protein Interaction Network][STRING DB]

[Protein-Protein Interaction Network][STRING DB] 0 I want to reconstruct Protein-Protein Interaction Network of some Bacterial strains using STRING DB. I have proteome datasets of these bacterial strains. But these strains are not listed in STRING DB. How can I proceed further? Please guide me from basics. Thanks. proteome PPI bacteria…

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Purpose, Principles, Applications and more

DNA sequencing is a laboratory technique used to determine the order of nucleotides (adenine, cytosine, guanine, and thymine) in a DNA molecule. It is a fundamental tool in molecular biology and genetics, with a wide range of applications in fields such as genomics, medicine, forensics, and evolutionary biology. There are…

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KRTA6A and FA2H Are Hub Genes Associated With Cgas-STING-related Immunogenic Cell Death in Lung Adenocarcinoma

Abstract Background/Aim: The immunogenic cell death (ICD) pathway plays a crucial prognostic role in lung adenocarcinoma (LUAD) therapy. The cyclic GMP–AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway is an upstream mechanism that drives ICD activation, but the interaction of hub genes remains unclear. The present study aimed to investigate…

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Reveal the potential molecular mechanism of circRNA regulating immune-related mRNA through sponge miRNA in the occurrence and immune regulation of papillary thyroid cancer

Background: Papillary thyroid cancer (PTC) is the most common endocrine malignant tumour. The purpose of this study was to explore the potential molecular mechanism of circRNA regulating immune-related mRNA through sponge miRNA in the occurrence and immune regulation of PTC. Methods: All data were downloaded from public databases, such as…

Continue Reading Reveal the potential molecular mechanism of circRNA regulating immune-related mRNA through sponge miRNA in the occurrence and immune regulation of papillary thyroid cancer

Design of Cyclic Peptides Targeting Protein-Protein Interactions using AlphaFold

Abstract More than 930,000 protein-protein interactions (PPIs) have been identified in recent years, but their physicochemical properties differ from conventional drug targets, complicating the use of conventional small molecules as modalities. Cyclic peptides are a promising modality for targeting protein-protein interactions (PPIs), but it is difficult to predict the structure…

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Cloud costs continue to rise among IT commodities

The U.S. government’s inflation index recorded the highest-ever reading for a technology category that includes cloud computing, which has become a core component of enterprise IT strategies. The Producer Price Index (PPI) for July, released late last week, reported a year-over-year price hike of 2.8% for data processing, hosting…

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The Role of Artificial Intelligence in Protein-Protein Interaction Analysis

Exploring the Role of Artificial Intelligence in Protein-Protein Interaction Analysis The field of bioinformatics is witnessing a revolution, thanks to the advent of artificial intelligence (AI). A prime example of this revolution is the role of AI in protein-protein interaction (PPI) analysis. The complex nature of PPIs, which play a…

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Bioinformatics analysis of hedgehog interacting protein in colorectal cancer: a study based on GEO data and TCGA data | BMC Gastroenterology

HHIP was lowly expressed in CRC tissues and HHIP expression was associated with cancer patient prognosis We acquired the RNA-sequencing data of CRC from TCGA public database. To pursue possible roles of HHIP in carcinostasis, we first analyzed HHIP expression in 33 types of human cancers. As shown in Fig. 1A,…

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Stock market today: Live updates

Traders work on the floor of the New York Stock Exchange. NYSE Stock futures rose on Thursday morning as Wall Street looked ahead to a key inflation reading that could impact the Federal Reserve’s next rate move. Futures tied to the Dow Jones Industrial Average rose 152 points, or 0.43%….

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Matlab PANDA function issues

Matlab PANDA function issues 0 I’m utilizing this site’s guidelines to run PANDA through Matlab (but I also had to make a couple edits because I don’t have ppi to use; I was told, though, that ppi isn’t required and Matlab should be simple to use for that purpose). Here…

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Stock Traders Shun Risk in Run-Up to Key CPI Test: Markets Wrap

Breadcrumb Trail Links PMN Business A slide in big tech and higher energy prices weighed on Wall Street sentiment ahead of inflation data that will help shape the outlook for the Federal Reserve’s next steps. Author of the article: Bloomberg News Rita Nazareth Published Aug 09, 2023  •  Last updated…

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Bioconductor – BioNAR

DOI: 10.18129/B9.bioc.BioNAR   Biological Network Analysis in R Bioconductor version: Release (3.17) the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of…

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Leveraging AI to Uncover the Secrets of Protein-Protein Interactions

Unlocking the Mysteries of Protein-Protein Interactions through AI Technology Protein-protein interactions (PPIs) are fundamental to virtually all biological processes. They form the basis for cellular functions, from DNA replication to cell division, and are critical to understanding the mechanisms of diseases. However, deciphering the complex network of PPIs has been…

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differential expression – Using PANDA to infer gene regulatory networks without ppi

I’m using this tutorial (github.com/netZoo/netZooM/blob/master/tutorials/panda/panda.pdf) to use PANDA to infer gene regulatory networks, but without ppi values (which I’ve been told can be done easily using MATLAB). I replicated the codes given in the tutorial but I omitted all the portions with ppi. After doing so, I’m getting a lot…

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A systems biology approach to pathogenesis of gastric cancer: gene network modeling and pathway analysis | BMC Gastroenterology

In recent years, different investigations in the area of multi-center genomics research from gene to systems level and next-generation sequencing, clarified the various mechanisms specifically involved in the tumor progression [29]. This study used bioinformatics analysis to further investigate the genes involved in GC pathogenesis. In addition, the current study…

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Integrated analysis of circRNA, lncRNA, miRNA and mRNA to reveal the ceRNA regulatory network of postnatal skeletal muscle development in Ningxiang pig

Introduction: The development of skeletal muscle is regulated by regulatory factors of genes and non-coding RNAs (ncRNAs). Methods: The objective of this study was to understand the transformation of muscle fiber type in the longissimus dorsi muscle of male Ningxiang pigs at four different growth stages (30, 90, 150, and…

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A multiplexed time-resolved fluorescence resonance energy transfer ultrahigh-throughput screening assay for targeting SMAD4-SMAD3-DNA complex

Abstract The signaling pathway of transforming growth factor-beta (TGFβ) plays crucial roles in the establishment of an immunosuppressive tumor microenvironment, making anti-TGFb; agents a significant area of interest in cancer immunotherapy. However, the clinical translation of current anti-TGFb; agents that target upstream cytokines and receptors remains challenging. Therefore, the development…

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Biomolecules | Free Full-Text | Genome-Wide Acetylation Modification of H3K27ac in Bovine Rumen Cell Following Butyrate Exposure

1. Introduction The digestive tract greatly influences the maintenance of energy requirements in cattle due to its crucial role in digesting and absorbing nutrients. The rumen is an essential organ in the digestive tract for feed efficiency, with relatively high metabolic activities. The digestion of solid-feeding materials generates short-chain fatty…

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Reduced Vrk2 expression is associated with higher risk of depression in humans and mediates depressive-like behaviors in mice | BMC Medicine

The strategy and logic of choosing VRK2 SNPs for genetic analyses We retrieved the summary statistics of VRK2 SNPs in 23andMe, UK Biobank, and PGC2 samples [2, 3], and 256 SNPs region were available in all three GWAS datasets (a total of 246,363 cases and 561,190 controls). An overview about…

Continue Reading Reduced Vrk2 expression is associated with higher risk of depression in humans and mediates depressive-like behaviors in mice | BMC Medicine

GPX4 is a key ferroptosis biomarker and correlated with immune cell populations and immune checkpoints in childhood sepsis

Identification of DE-FRGs in sepsis After the debatch normalization treatment of GSE26378 and GSE26440 (Fig. 2A, Supplementary Figure 1), the differential expression analysis was performed, including 20,021 significantly differentially expressed genes, including 12,758 upregulated genes and 7,263 downregulated genes. log2FC ≥ 1, adjusted P < 0.05 (Fig. 2B). To explore differentially expressed FRG in sepsis, we extracted…

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Can you recommend me a database of bacterial gene essentiality?

To find what you need, ask you question in this form In NCBI: ‘database containing essential genes of gut bacteria’ I’ve got a lot of articles. For example: www.ncbi.nlm.nih.gov/pmc/articles/PMC5711816/pdf/fmicb-08-02331.pdf A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes Chong Peng1, Yan Lin1, Hao Luo1 and Feng…

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How do I correctly format this line for PandaR?

How do I correctly format this line for PandaR? 0 I’m trying to implement the panda function for the dataframe I’m using (and I have tried to convert it into a list, but the result is the same). I’m using this guide: www.bioconductor.org/packages/devel/bioc/vignettes/pandaR/inst/doc/pandaR.html Here is my code: pandaResult <- panda(pandaToyData$Name,…

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Homozygosity mapping in the Kazakh national dog breed Tazy

In this study, for the first time, we presented an overview of the ROH patterns of the Kazakh national dog breed Tazy from a genome-wide perspective. According to the obtained results, there was strong evidence of distant inbreeding in this breed about 50 generations ago, as most ROH fell into…

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How to merge BLE_UART and Aes_ctr project file – Nordic Q&A – Nordic DevZone

Hello, I have two project one is Ble UART and second AES_ctr, i want to combine AES_ctr project and sdk_config.h file into BLE_UART ,so i can use AES API in BLE UART code can you guide me how to start it. <!DOCTYPE CrossStudio_Project_File> <solution Name=”nrf_crypto_aes_ctr_pca10056″ target=”8″ version=”2″> <project Name=”nrf_crypto_aes_ctr_pca10056″> <configuration …

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Integrated bioinformatics and wet-lab analysis revealed cell adhesion prominent genes CDC42, TAGLN and GSN as prognostic biomarkers in colonic-polyp lesions

Clinicopathological characteristics of patients with pre-cancerous lesions Clinicopathological features of the 20 included patients with colon polyps were extracted from their files and presented at the beginning of the survey. All resected samples were categorized into high-risk and low-risk polyps based on reported pathological feature of the samples. The mean…

Continue Reading Integrated bioinformatics and wet-lab analysis revealed cell adhesion prominent genes CDC42, TAGLN and GSN as prognostic biomarkers in colonic-polyp lesions

Integrated analysis of CircRNA, lncRNA, miRNA and mRNA to reveal the ceRNA regulatory network of postnatal skeletal muscle development in Ninxiang pig

Gang z. Yu1, li x. xu1, nini ai1, ming k. wang1, wen p. zhang1, tong x. li1, sui liufu1, lin x. liu1, Jun Jiang1, Jingjing Gu1, Ning Gao1 and Haiming Ma1* 1Hunan Agricultural University, China The final, formatted version of the article will be published soon. …

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Accutar Biotechnology Announces First Patient Dosed with AC0676 in Phase 1 Study in Patients with Relapsed/Refractory B-cell Malignancies

– Chimeric Degrader With a Differentiated Mechanism of Action vs. BTK Inhibitors by Removing Both Kinase And Scaffolding Functions of BTK – – Broad BTK Mutant Coverage Designed to Overcome Resistance to Covalent And Non-Covalent BTK Inhibitors – – Improved Selectivity Profile Sparing Common Off-Targets Observed for BTK Inhibitors –…

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Identification of macrophage-related genes in sepsis-induced ARDS using bioinformatics and machine learning

Screening of differentially expressed genes in GSE32707 According to the screening criteria of differentially expressed genes, there were 489 differentially expressed genes between the control and sepsis groups, of which 152 genes were downregulated in sepsis patients and 337 genes were upregulated in sepsis patients (Fig. 1A). In contrast, there were…

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CD44 is a potential immunotherapeutic target and affects macrophage infiltration leading to poor prognosis

The role of CD44 in tumorigenesis and as a prognostic marker in BLCA In this study, we determined CD44 mRNA expression in normal and in tumor tissues for BLCA via the use of the TIMER database (Fig. 1A). Our analysis found that there was a significant difference in the expression of…

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Examining TET2/ASXL1 and Core Mutations DNA Methylation Profile in MDS

The following is a summary of “Analysis of core mutation and TET2/ASXL1 mutations DNA methylation profile in myelodysplastic syndrome,” published in the June 2023 issue of Hematology by Feng, et al. For a study on myelodysplastic syndromes (MDS), researchers sought to analyze genetic mutations and clinical characteristics and examine their…

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IJMS | Free Full-Text | Analysis of CircRNA Expression in Peripheral Blood of Holstein Cows in Response to Heat Stress

1. Introduction With the global temperature rise, the dairy industry is confronted with a significant challenge brought about by severely damaging impacts of heat stress. Heat stress increases mortality rates and threatens the health of livestock, especially in highly productive and intolerant species. The increase in ambient temperature–humidity index (THI)…

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ENPP1 Immunobiology as a Therapeutic Target | Clinical Cancer Research

Figure 1. ATP–Ado extracellular metabolism and elicited signaling through adenosinergic receptors. A, Canonical and noncanonical extracellular receptors contributing to the hydrolysis of ATP and other metabolites. In the TME, two different yet partially overlapping pathways mediate the hydrolysis of ATP to adenosine (Ado). In the noncanonical pathway, Ado can be…

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How to successfully upload gene expression data in DyNetViewer

How to successfully upload gene expression data in DyNetViewer 0 I need to construct a dynamic PPI interaction analysis using gene expression data from three time points. I have this cytoscape app called DyNetViewer which requires me to put the data in a txt file before uploading it. I have…

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DyNetViewer

DyNetViewer 0 I need to construct a dynamic PPI interaction analysis using gene expression data from three time points. I have this cytoscape app called DyNetViewer which requires me to put the data in a txt file before uploading it. I have my data in txt file but it gives…

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Med-Life Discoveries to start rare pediatric disease trial

Med-Life Discoveries, LP (MLD) is a Canadian biopharmaceutical company dedicated to advancing a therapy to reduce symptoms for a devastating pediatric rare disease, Rhizomelic chondrodysplasia punctata (RCDP), which causes significant physical and neurological delays in children who inherit it.  MLD has received a no objection letter (NOL) from Health Canada…

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Comprehensive analysis of the coding and non-coding RNA transcriptome expression profiles of hippocampus tissue in tx-J animal model of Wilson’s disease

Behavioral testing After undergoing a four-day training program, the mice were subjected to a positioning cruise experiment on the fifth day. The experiment involved comparing the escape latency and swimming distance in the quadrant opposite to the platform between the WD group and the control group. The findings indicated that…

Continue Reading Comprehensive analysis of the coding and non-coding RNA transcriptome expression profiles of hippocampus tissue in tx-J animal model of Wilson’s disease

DeepMind’s AlphaFold Seeing Uptake for Protein-Protein Interaction Work

NEW YORK – Since its introduction in 2018, DeepMind’s AlphaFold program has become a key tool in biological research, allowing scientists to predict protein structures with high accuracy based on their amino acid sequences. More recently, researchers have begun using AlphaFold and its newer iteration, AlphaFold2, for protein-protein interaction (PPI)…

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De novo protein design by inversion of the AlphaFold structure prediction network

Abstract De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in computational design strategies, de novo design of protein structures remains challenging, given the vast size…

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Three genes expressed in relation to lipid metabolism considered as potential biomarkers for the diagnosis and treatment of diabetic peripheral neuropathy

Screening for pivotal genes in diabetic peripheral neuropathy In screening the DEGs, a total of 6 DPN samples and 6 control samples were included in the GEO dataset GSE95849, and this dataset was normalised. A principal component analysis (PCA) of GSE95849 was conducted to demonstrate clustering using scatter plots. Each…

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Human bone marrow-derived mesenchymal stem overexpressing microRNA-124-3p inhibit DLBCL progression by downregulating the NFATc1/cMYC pathway | Stem Cell Research & Therapy

Microarray-based expression analysis and GEO database analysis The DLBCL-related miRNA expression profiles of GSE29493 and GSE40239 were retrieved from the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/). MiR-124’s pan cancer analysis is conducted through online websites (www.picb.ac.cn/dbDEMC/). Bioinformatics predicted NFATc1 as the target of miR-124-3p The miRbase (www.mirbase.org/), miRDB (mirdb.org), and…

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Using Apache Age for Bioinformatics: Exploring Protein-Protein Interaction Networks

The field of bioinformatics has rapidly evolved with the advent of high-throughput sequencing technologies and other advanced experimental methods. These technologies generate massive datasets that require equally advanced computational methods for analysis. Graph databases, such as Apache Age, have emerged as powerful tools for managing and analyzing these complex datasets….

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Pinostrobin, a fingerroot compound, regulates miR-181b-5p and induces acute leukemic cell apoptosis

Leukemia cell culture The human acute promyelocytic leukemia cell line (NB4) and the human acute lymphocytic leukemia cell line (MOLT-4) were purchased from Cell Lines Service (Eppelheim, Germany). Leukemia cells were cultured in RPMI-1640 medium supplemented with 10% (v/v) FBS and 1% (v/v) penicillin–streptomycin (Gibco Life Technologies, Waltham, MA, USA)….

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Bioinformatics-Based Identification of CircRNA-MicroRNA-mRNA Network for Calcific Aortic Valve Disease

Background. Calcific aortic valve disease (CAVD) is the most common native valve disease. Valvular interstitial cell (VIC) osteogenic differentiation and valvular endothelial cell (VEC) dysfunction are key steps in CAVD progression. Circular RNA (circRNAs) is involved in regulating osteogenic differentiation with mesenchymal cells and is associated with multiple disease progression,…

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Bioconductor – magrene (development version)

DOI: 10.18129/B9.bioc.magrene   This is the development version of magrene; for the stable release version, see magrene. Motif Analysis In Gene Regulatory Networks Bioconductor version: Development (3.18) magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan…

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Bioinformatics Analysis of Differentially Expressed Genes in Ischemic Cardiomyopathy Using GEO Database

It was to analyze differentially expressed genes and their expression characteristics in ischemic cardiomyopathy (ICM) by bioinformatics and provide targets for drug therapy of ICM. For this purpose, the gene expression data of ICM in the gene expression omnibus (GEO) database were used, the differentially expressed genes between healthy myocardium…

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Travere Therapeutics Announces Topline Results from

The DUPLEX Study did not achieve the primary efficacy eGFR slope endpoint over 108 weeks of treatment Secondary and topline exploratory endpoints trended favorably for sparsentan Treatment with sparsentan resulted in a reduction of proteinuria that was sustained through 108 weeks of treatment Sparsentan was well-tolerated with a consistent safety…

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Hidden RNA repair mechanism discovered in humans

RNA ligase mechanism and identification of C12orf29 by chemical proteomics using modified Ap3A probe. a Schematic display of the three-step mechanism of RNA ligation by a 5′–3′ RNA ligase. In step 1, the ligase is auto-AMPylated on the catalytic lysine using ATP as the co-substrate. In step 2, the AMP…

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Presentation_1_Genetic variations in the retrograde endocannabinoid signaling pathway in Chinese patients with major depressive disorder.pdf

Background The retrograde endocannabinoid (eCB) pathway is closely associated with the etiology of major depressive disorder (MDD) at both pathophysiological and genetic levels. This study aimed to investigate the potential role of genetic mutations in the eCB pathway and underlying mechanisms in Han Chinese patients with MDD. Methods A total…

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Bioinformatics analysis of the pathogenic link between Epstein-Barr virus infection, systemic lupus erythematosus and diffuse large B cell lymphoma

Epstein-Barr virus (EBV) is a risk factor for diffuse large B-cell lymphoma (DLBCL) and systemic lupus erythematosus (SLE). While prior research has suggested a potential correlation between SLE and DLBCL, the molecular mechanisms remain unclear. The present study aimed to explore the contribution of EBV infection to the pathogenesis of…

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Screening and identification of key biomarkers in diabetic kidney disease and its complications: Evidence from bioinformatics and next generation sequencing data analysis

Abstract Diabetic patients are prone to diabetic kidney disease (DKD), which may cause cardiovascular damage, hypertension and obesity, and reduce quality of life. As a result, the life quality of patients was seriously reduced. However, the pathogenesis of diabetic kidney disease (DKD) has not been fully elucidated, and current treatments…

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Expression profile of PRGs in gout patients

Introduction Gout is an inflammatory disease caused by the deposition of monosodium urate (MSU) crystals in joints and other non-joint tissues. The main clinical manifestations of gout include recurrent joint redness, swelling, heat and pain, and even joint mutilation, urinary acid nephropathy and renal failure.1,2 The incidence and prevalence of…

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Diagnostic signatures in Ischemic cardiomyopathy patients

Introduction Ischemic cardiomyopathy (ICM), characterized by high mobility and high mortality, is so far one of the most prevalent etiologies of congestive heart failure.1 The development of left ventricular (LV) systolic dysfunction, which is typically brought on by prior acute myocardial infarction(s), or, alternatively, a sneaky process of gradual deterioration…

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New nanomedicine can suppress tumors by turning ‘cold’ tumors into ‘hot’ ones

*For medical professionals to read and reference only Recently, the team of Dean Li Jie of the Oncology Department of Guang’anmen Hospital, China Academy of Chinese Medical Sciences , based on the immune effect of papaya saponin I, developed a new nano-drug that can achieve efficient tumor suppression by converting…

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Nanoparticle-based combination therapy for ovarian cancer

Introduction Ovarian cancer is one of the most common gynecologic malignancies with high morbidity.1 Due to its relatively asymptomatic nature, about 70% of patients are diagnosed at an advanced stage and have poor prognosis, leading to high mortality rates.2,3 The clinical treatment of ovarian cancer mainly relies on chemotherapy after…

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Molecular pathways identified from single nucleotide polymorphisms demonstrate mechanistic differences in systemic lupus erythematosus patients of Asian and European ancestry

Identification of ancestry-dependent and independent non-HLA SLE-associated variants and downstream target genes Despite the success achieved by GWAS in mapping polygenic disease risk loci in SLE, the biological implications of the majority of identified variants has remained unknown. To gain a broader view of how inherited genetic variation impacts disease…

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Travere Therapeutics Reports Publication of Interim Analysis from the Phase 3 PROTECT Study of FILSPARI By Investing.com

Travere Therapeutics, Inc. (TVTX) today announced publication in The Lancet of the interim analysis of efficacy and safety data from the ongoing pivotal, Phase 3 PROTECT Study evaluating FILSPARI™ (sparsentan) in adults with IgA nephropathy (IgAN). The data are simultaneously being presented in a late-breaking trials session at the World…

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enriched genes PPI network

enriched genes PPI network 1 It doesn’t work like that. Wherever you obtained Figure 1, it is obvious that it wasn’t done by STRING, as its style and format are completely different. If I were to guess, what’s in Figure 1 appears to be old results that were plotted manually….

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Analysis of Molecular Mechanism between COPD and osteporosis

Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic respiratory condition that mostly occurs in middle-aged and elderly people. COPD manifests as a progressive airflow limitation associated with an abnormal lung inflammatory response.1 As a disease with high incidence, disability rate, long disease course, and multiple comorbidities, COPD has…

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Trying to make a Mauve alignment with 2 sequences and keep getting error code 3

Trying to make a Mauve alignment with 2 sequences and keep getting error code 3 1 I’m trying to create an alignment with two sequences in Mauve (Windows) and keep getting error code 3. I tried using different formats for my sequences, but that didn’t seem to change anything. I…

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Identification of novel prognostic targets in coronary artery disease and related complications using bioinformatics and next generation sequencing data analysis

Abstract Coronary artery disease (CAD) is the most common cardiovascular disorder and the leading cause of heart-related deaths in world. Increasing molecular targets have been discovered for CAD and CAD – related complications prognosis and therapy. However, there is still an urgent need to identify novel biomarkers. Therefore, we evaluated…

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